dbSNP rs11564258: MUC19:c.85+587G>A (chr12-40398498-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000454784.10(MUC19):c.85+587G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0328 in 152,266 control chromosomes in the GnomAD database, including 231 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.033 ( 231 hom., cov: 32)

Exomes 𝑓: 0.013 ( 0 hom. )

Consequence

MUC19
ENST00000454784.10 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.722

Publications

64 publications found

Variant links:

Genes affected

MUC19 (HGNC:14362): (mucin 19, oligomeric) This gene encodes a member of the gel-forming mucin protein family. Mucin family members are glycoproteins that have tandem repeats which are extensively O-glycosylated. The structural features of mucin proteins are responsible for the gel-like properties of mucus. The encoded protein may be involved in disruption of the ocular surface in Sjogren syndrome. [provided by RefSeq, Apr 2014]

MUC19 links:

ENSG00000258167 (HGNC:):

ENSG00000258167 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
MUC19	NM_173600.2 link	c.85+587G>A	intron_variant	Intron 2 of 171	NP_775871.2	Q7Z5P9-1
LOC105369736	XR_007063562.1 link	n.305-2512C>T	intron_variant	Intron 3 of 4
LOC105369736	XR_944866.1 link	n.409+62C>T	intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC19	ENST00000454784.10 link	c.85+587G>A		intron_variant	Intron 2 of 172	5		ENSP00000508949.1

Frequencies

GnomAD3 genomes

AF:

0.0328

AC:

4990

AN:

152068

Hom.:

230

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00770

Gnomad AMI

AF:

0.0526

Gnomad AMR

AF:

0.117

Gnomad ASJ

AF:

0.0582

Gnomad EAS

AF:

0.0398

Gnomad SAS

AF:

0.107

Gnomad FIN

AF:

0.0290

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0218

Gnomad OTH

AF:

0.0440

GnomAD4 exome

AF:

0.0125

AC:

AN:

Hom.:

AF XY:

0.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0156

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0328

AC:

4996

AN:

152186

Hom.:

231

Cov.:

AF XY:

0.0365

AC XY:

2713

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.00768

AC:

319

AN:

41558

American (AMR)

AF:

0.118

AC:

1798

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.0582

AC:

202

AN:

3472

East Asian (EAS)

AF:

0.0397

AC:

206

AN:

5184

South Asian (SAS)

AF:

0.108

AC:

520

AN:

4818

European-Finnish (FIN)

AF:

0.0290

AC:

307

AN:

10600

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0218

AC:

1479

AN:

67972

Other (OTH)

AF:

0.0435

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

221

442

662

883

1104

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

186

248

310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0281

Hom.:

445

Bravo

AF:

0.0390

Asia WGS

AF:

0.0860

AC:

297

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.21

(source)

DANN

Benign

0.36

PhyloP100

-0.72

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over